Runes and Ruins
by shortcomings
Summary: Jonathan Fairchild and his sister Clary, along with their friends, the Lightwoods, have grown up in a country plagued by war. They're used to running and hiding and having to fend for themselves while their parents are gone. But when Valentine and his Circle are gaining power, what are the chances of survival for a small group of teens?


**Guess who finally got around to rewriting this piece of junk? Or at least chapter one of it?**

 **Just in case you've forgotten or are a new reader, let me clarify a few things: I based this story off quite a few 'what ifs' I had. What if Valentine had never experimented on any of his children? What if Maryse had helped Jocelyn betray the Circle? What if Robert had left Maryse? What if Jocelyn hadn't fled Idris and decided to raise Jonathan and Clary as shadowhunters? What if Jon and Clary practically grew up with the Lightwoods and Jace? What if Valentine hadn't faked his death and he and the Circle were actively waging war against the Clave?**

 **Disclaimer: If I owned any of the characters and/or original plot it probably would've been very different from the series we all know and love.**

* * *

"Jon."

Jonathan Fairchild glanced up from the current hardback he was reading. His younger sister, Clary, was standing in the doorway of his room, pale-faced and tense.

"What's wrong?" He asked. Jon set down his book, swung legs off his bed, and stood up. Possible scenarios, none of them good, ran through his head as he debated what had startled Clary.

She pushed a few strands of red hair out of her eyes. "Circle members," she said. She didn't sound scared, but fear was written into her rigid posture and the nervous tapping of her nails against the door frame.

"How far?" Jon wasn't at all surprised by her response. What else could it be? The Circle of Raziel was the only real threat in Idris.

His sister shrugged. "I'm not the best judge of distance. Just close enough to distinguish specks of black as men on horses."

He sighed. "Just close enough that we have enough time to saddle Wayfarer and Shadow and disappear into the forest if they're cantering."

Clary nodded and Jon sighed again. "I'll head down to the stable and start tacking up Nyx and Wayfarer, you go grab some weapons while I do that." Clary gave him another curt nod before turning and darting off to do as her older brother had instructed.

Jon cast a glance around his room, making sure he wasn't leaving anything important behind, before following his younger sister out of the room.

* * *

Jon had just finished cinching the saddle on a black mare when Clary hurried into stable, a short sword sheathed at her hip and Jon's broadsword tucked in its scabbard grasped in her hand. She handed the blade to the blond boy. "You're on Wayfarer, I'm on Nyx?" She asked.

"Yeah. You need help getting into the saddle?" The last bit was teasing, an attempt to lighten the mood.

Clary briefly flashed him an obscene gesture as she strode over to the black mare. "I'm not helpless." She placed her foot in the stirrup and swung herself up into the saddle.

"You've been spending too much time with Jace."

Clary raised her eyebrows in an "oh really" expression. They were both friends with Jace, though Jon was most definitely closer to him. "Are you just going to stand there?" She asked impatiently. "I don't know if you've noticed, but we don't exactly have all the time in the world."

Jon rolled his eyes at her, well, Clary-like attitude. He walked over to a black and white stallion standing a few feet from Nyx. With quick, effortless grace he placed his foot in the stirrup and swung up into the saddle. A second later and his other foot was wedged in its respective stirrup and the reins were firmly grasped in his slender hands. "Ladies first," he said, gesturing towards the open stable door. "As you said, we don't have all the time in the world."

Clary huffed a response and nudged Nyx forward into a walk. As soon as the mare stepped out of the stable Clary was nudging her into a trot and Jon was urging Wayfarer after her. Soon they were both cantering.

They'd only been riding for a quarter hour before Clary twisted around her in her saddle to look back at him and pointed up at the sky. Following the direction of her index finger, Jon's green eyes looked at the sky.

Shit.

Dark storm clouds were beginning to gather above them- quickly too. In the hour it would take them to get the Lightwood's it would definitely start raining. It wouldn't just rain though, it would be an all out storm. That would slow them down a bit, if Clary wasn't riding Nyx. Clary could control her in normal weather, even during heavy rain. As soon as strong wind, thunder, or lightning entered the picture, however, Nyx became a skittish nightmare- difficult even for Jon control.

His gaze flickered back to Clary, who'd turned back around in her saddle. "It's still moving. It might not hit us," he called.

"It's moving the same direction as us," Clary shouted back. "We can't outrun it either."

"Are going to be okay on Nyx?"

"Why wouldn't I be?" She asked stubbornly. "I've ridden her several times before."

"We can stop and switch horses."

"I. Can. Handle. Her."

Jon decided that arguing further was pointless. Clary could make the most stubborn of mules look downright cooperable when someone wasn't challenging what she was and wasn't capable of. He'd have better luck trying to persuade the sky to turn green.

Only a handful of minutes passed before a steady drizzle began falling from the clouds. A minute or two later and it began to come down in a fierce deluge. Lightning forked down to kiss the ground for fraction of second and was quickly followed by a deafening boom of thunder.

Nyx skidded to a stop on the slippery rocks. A high whinny cut through the rain as the mare tossed her head and pranced skittishly. Jon tugged on Wayfarer's reins, bringing him to a stop and prepared to dismount to help Clary with Nyx if she couldn't get her back under control. Clary was bent over the mare's neck, slowly stroking her neck and murmuring soothing words that were lost in the tumult of the storm. Her hair hung down in a wet curtain around her face, the usual flaming color darkened to a bloodier tone.

Time seemed to slow as Jon distantly heard another clap of thunder. Nyx reared up with a shrill cry. Clary lost her balance. Everything was muted except for Clary's own terrified shriek as she slowly -ever so slowly- tumbled to the ground. Time seemed to return to its normal speed as her tiny form landed in a crumpled heap on the rocks.

"Clary!" Jon dismounted Wayfarer and darted over to where his sister lay unconscious. Her left leg was bent awkwardly, a splash of blood stained the leg of her jeans where the jagged edge of a rock must have cut a small gash just beneath her knee, there was small scrape on her forehead half concealed by the way she'd landed on her side. Other than that -thank Raziel- she looked fine. He couldn't tell if she'd suffered a concussion or something along the lines of that, but she hadn't broken her neck and that was enough.

Jon hastily pulled out his stele and traced an iratze onto Clary's neck. As the swirling lines went from burned red to inky black before sinking slowly into her skin he slipped his arms underneath his unconscious sister and lifted her up.

What was he going to do with Nyx? He could tie her reins to Wayfarer's saddle, but that slow them down considerably. Not to mention it could be dangerous if she jerked too violently. Maybe Nyx would follow if he started riding away on Wayfarer. He didn't see any other option.

Sighing, he strode back over to Wayfarer and after a few attempts managed to get Clary to stay up in the front of the saddle long enough for him to swing up onto the stallion's back. He gathered the reins in his hands and nudged Wayfarer into motion.

* * *

Alec Lightwood must have seen them coming at least a few minutes before they arrived, because he was standing just outside the manor when they arrived. He was wearing a dark blue raincoat. The hood was pulled down low over his head, making his expression hard to read. "I'll...Clary...empty...in...stables," was all Jon managed to catch over the storm. He slid from the saddle and caught Clary as she began to fall off Wayfarer's back. Alec gently eased Clary into his own arms. He stood there for a moment studying her limp form before turning and walking into the manor.

Jon watched him for a second before turning to grab Wayfarer's and Nyx's, who as he had hoped galloped closely behind Wayfarer afraid of being alone in the rain, reins and led them into the stable. He spent the next half hour untacking the two equines, brushing them down, and making sure they had water and bucket of feed.

He was reluctant to step back into the raging storm, and set a brisk jog the dozen or so yards to the manor house. The architecture had been around for centuries and had belonged to Lightwood family almost as long as it had been standing. When Robert Lightwood left his wife and children he allowed them to keep the property, mainly because he had never liked it in the first place.

Reaching the doorstep, Jon let himself into the house. Waiting for him the foyer with a towel and a change of dry clothes was Isabelle Lightwood, a tall raven-haired sixteen year-old girl with eyes nearly as dark as her hair. "You're soaked," she stated as her dark gaze skimmed over him. She held out the stack of folded clothes and towel. "Here. Alec's clothes should fit you all right. When you're done changing Clary's in her normal room."

He took the towel and clothes. "Thanks, Izzy." He flashed her a grateful smile.

She shrugged. "Alec originally told Jace to gather up some stuff, but he was being an ass."

Jon chuckled. Jace Herondale, in adition to being one of Jon's closest friends, had been raised along with Alec, Isabelle, and their younger brother Max since birth. He was just a matter of months older than Clary and Isabelle and almost intolerably arrogant on the best of days. "That sounds like Jace."

Isabelle shrugged again. "I'm going to check on Clary. You better dry up before that puddle gets any bigger." She turned and marched off to the staircase.

Jon glanced down at his feet. There was, indeed, a small puddle forming around his feet. "I guess I better mop this up when I'm done, huh?" he asked himself with a sheepish smile.

"Let Jace get it," called Izzy as she disappeared up to the second floor.

Jon shrugged to no one in particular and trudged off to the first floor bathroom to change.

"How's Clary?" Jon asked as he slipped into Clary's room. His sister was propped up slightly by a couple of pillows and appeared to be sleeping peacefully. Isabelle was curled beside her on the double bed and was dividing her damp red curls into three sections for a braid; a wide toothed comb lay discarded by the taller girl's feet.

"She's fine. I gave her another iratze which seemed to pretty much do the trick." In his initial scan of the room Jon hadn't seen Alec and now was surprised to hear him speak. His gaze flickered over to the far corner of the room and landed on his best friend. Gone was the raincoat and low-drawn hood that concealed his features. Alec Lightwood in all appearances was a male version of Isabelle- tall, slender, pale-skinned, with inky black hair, winged eyebrows,and an elegant, well-structured face. Unlike Isabelle, though, Alec's eyes were a vivid, entrancing blue that begged to noticed and were at constant odds with his withdrawn personality. "She'll probably be rather sore when wakes though, especially her leg and head."

"Did she ever wake up?" Jon asked, moving out of the doorway to stand at the foot of Clary's bed.

Alec nodded. "For a few minutes. She looked pretty tired so I told her to go ahead and go to sleep for tonight." He pushed a bit of hair out of his eyes. "What happened by the way? Your mom told you guys to stay at your place until she got back unless something happened."

"Circle members were nearing the house. I don't think they were coming for a cup of tea and some gossip either. We left as soon as Clary spotted them and while we might've gotten away in time we weren't able to outrun the storm. Nyx panicked and dumped Clary on the rocks."

"Ouch." Izzy commented as she began weaving sleeping Clary's hair into braid, finally satisfied that she'd evenly divided the curls.

"So how long do you think you'll stay?"

Jon opened his mouth to respond but was cut off when Alec spoke again. "Oh, look." His gaze traveled to the door. "The family's all here now." Jon looked over his shoulder to see Jace and the youngest Lightwood, nine year-old Max, standing in the doorway.

"What happened to Clare?" Max asked pushing his too big glasses up his nose. For some reason when Max was learning to talk he'd shortened Clary to Clare and it had stuck as his special nickname for her.

Jon smiled affectionately down at the grey-eyed kid. "She fell and broke her leg. She's resting now."

"But it's not night," Max protested. "Couldn't she have waited a few hours so we could play?"

Jon's smile grew into a grin. Max was so sweet and innocent that even Jace was nice to him. "But she's really, really tired and decided she doesn't care if it's not night. She'll definitely want to play with you tomorrow when she wakes up."

"Can I go ahead and wake her up now?"

This time it was Jace who answered. "Not unless you want her to attack with one of her sketchbooks. You know how Clary is about her beauty sleep."

Max frowned. "Clare doesn't need any beauty sleep, though. She's pretty enough. And besides," he added. "Clare loves me. She wouldn't hit me."

Jace grinned and ruffled the small boy's hair. "The naivety of youth."

* * *

 **So what did everyone think of Chapter 1? Horrible? Great? Not bad, but not good either? Let me know in review, and I''ll see what I can do to improve.**

 **Also, I would like to note that between school, writing my own original novel, and soon soccer I will not be able to promise regular updates.**

 **Chapter 2 snippet**

Isabelle flipped her dark hair over her shoulder. "You need to hurry up and get dressed so we can go outside or wreck havoc in the basement like we usually do when you spend the night. We let you sleep in an extra thirty minutes because of your injuries-"

"How considerate. Your generosity never fails to touch."

 **xoxo- shortcomings**


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